{"bugs":[{"bugid":711818,"firstseen":"2025-07-11T02:48:40.189262","severity":"trivial","status":"IN_PROGRESS","summary":"sci-biology\/bwa: Buffer overflow (long prefix) in bns_fasta2bntseq, bns_dump (CVE-2019-11371)"}],"categories":[{"categoryid":450,"name":"dev-lang","summary":"The dev-lang category contains various programming language implementations and related tools."},{"categoryid":353,"name":"sci-biology","summary":"The sci-biology category contains software that can be used in biological and related scientific environments."},{"categoryid":396,"name":"virtual","summary":"The virtual category contains packages which satisfy virtual dependencies."}],"changelog":[{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"e09be1650bf1ab608446c80c6ac2835c083e91fe","committime":"2025-11-04T10:20:41","packageid":49132,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"mgorny@gentoo.org","authorname":"Michał Górny","body":"Done via:\n\n```\ngit grep -l 'virtual\/zlib\"' | xargs sed -i -e 's@virtual\/zlib\"@virtual\/zlib:=\"@'\n```\n\nSigned-off-by: Michał Górny ","commitid":"3f9689daa18058fa4adc944100fa1f95bfbaa5b4","committime":"2025-11-04T10:07:52","packageid":49132,"repoid":1,"summary":"*\/*: Use := on virtual\/zlib deps, part 6"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"5a1adb610b1d91ab6683cbe671e266f424224c16","committime":"2025-11-04T08:35:48","packageid":49132,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"mgorny@gentoo.org","authorname":"Michał Górny","body":"Update done using:\n\n```\ngit grep -l sys-libs\/zlib dev-* | xargs sed -i -e s@sys-libs\/zlib@virtual\/zlib@g\ngit diff --name-only | xargs copybump\ngit diff --name-only | xargs grep -l PYTHON_COMPAT | xargs gpy-impl -@dead\npkgcheck scan --commits -c SourcingCheck,VisibilityCheck --exit error\n```\n\nSigned-off-by: Michał Górny ","commitid":"f1351833569f8b22abc3dc9e74abeed7e8641096","committime":"2025-11-04T08:17:06","packageid":49132,"repoid":1,"summary":"sci-*\/*: update for virtual\/zlib"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"34218b8bb1520bf75c8f22fb7c5a3221415bc432","committime":"2025-03-25T04:20:13","packageid":49132,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"eschwartz@gentoo.org","authorname":"Eli Schwartz","body":"Signed-off-by: Eli Schwartz ","commitid":"771184da3c13e19b95b01a16bfa79dcf196db132","committime":"2025-03-25T04:10:05","packageid":49132,"repoid":1,"summary":"sci-biology\/bwa: note that filter-lto has been fixed upstream"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"3b8f7ac3f0acdb745d5dc71b988869551b83996b","committime":"2024-02-29T05:03:47","packageid":49132,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"eschwartz93@gmail.com","authorname":"Eli Schwartz","body":"Closes: https:\/\/bugs.gentoo.org\/862255\nSigned-off-by: Eli Schwartz \nSigned-off-by: Sam James ","commitid":"8479cf13101c1bcc4bf088768449a617f0146c8a","committime":"2024-02-29T04:26:03","packageid":49132,"repoid":1,"summary":"sci-biology\/bwa: mark as LTO-unsafe"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"d072618eb502f223a87bf54dda9de758c496f87b","committime":"2020-09-26T10:36:09","packageid":49132,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Package-Manager: Portage-3.0.8, Repoman-3.0.1\nSigned-off-by: David Seifert ","commitid":"1a7c939f8f1087c8031e2621e53bd3bda0f043af","committime":"2020-09-26T10:00:48","packageid":49132,"repoid":1,"summary":"sci-biology\/bwa: Remove old 0.7.16a"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Package-Manager: Portage-3.0.8, Repoman-3.0.1\nSigned-off-by: David Seifert ","commitid":"11e7107dfc5e8b95c3af3887c388fa1272b8ddb2","committime":"2020-09-26T10:00:45","packageid":49132,"repoid":1,"summary":"sci-biology\/bwa: Bump version to 0.7.17"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"f8bcddce7fdc2ca2c3df347114c56c970655d579","committime":"2020-01-25T19:45:38","packageid":49132,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Closes: https:\/\/bugs.gentoo.org\/706348\nPackage-Manager: Portage-2.3.85, Repoman-2.3.20\nSigned-off-by: David Seifert ","commitid":"71f83be9beeb1ed4c39d0e0ad442a8aba54a2c8c","committime":"2020-01-25T19:38:35","packageid":49132,"repoid":1,"summary":"sci-biology\/bwa: Fix -fno-common bug"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"299bb59f5cb803e437aa028d8dd5b082e923ab4f","committime":"2017-09-02T12:45:26","packageid":49132,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Package-Manager: Portage-2.3.8, Repoman-2.3.3\nCloses: https:\/\/github.com\/gentoo\/gentoo\/pull\/5593","commitid":"59716472229d52eacd4bba26ac2d90a9b3f44233","committime":"2017-09-02T11:07:41","packageid":49132,"repoid":1,"summary":"sci-biology\/bwa: Remove old"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"9504cbc4752f1f0328c395482b50bffc5f80ba8b","committime":"2017-09-02T08:23:53","packageid":49132,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Package-Manager: Portage-2.3.8, Repoman-2.3.3","commitid":"e04e78ab9f20899f699eb5c871dc77727deac3da","committime":"2017-09-02T08:07:02","packageid":49132,"repoid":1,"summary":"sci-biology\/bwa: Bump to 0.7.16a"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"25093d6359f778b8d1052f66ba9e26fc29ded21a","committime":"2017-02-28T20:35:29","packageid":49132,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"robbat2@gentoo.org","authorname":"Robin H. Johnson","body":"Signed-off-by: Robin H. Johnson ","commitid":"61b861acd7b49083dab687e133f30f3331cb7480","committime":"2017-02-28T19:47:27","packageid":49132,"repoid":1,"summary":"Drop $Id$ per council decision in bug #611234."},{"authoremail":"malfatti@neuro.ufrn.br","authorname":"T. Malfatti","commitid":"8457ba6f9fd6f0dbafcca1fb375788eeea02aae1","committime":"2017-01-26T18:44:34","packageid":49132,"repoid":1,"summary":"media-libs\/portaudio: Version bump"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"e4ece068dfce4ec8d08c6029584a201fd12ce72b","committime":"2017-01-21T02:04:50","packageid":49132,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"vapier@gentoo.org","authorname":"Mike Frysinger","commitid":"62fa24bb8afe5b4e83a853b62649cb5a7ae100f5","committime":"2017-01-21T01:52:40","packageid":49132,"repoid":1,"summary":"fix quoting to a lot of patch calls"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"c5838acba7181bcec8f278a85ea4e506026d541a","committime":"2016-09-03T09:02:46","packageid":49132,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Package-Manager: portage-2.3.0","commitid":"9574df41e529782826a9e6b32bdbac1678f47875","committime":"2016-09-03T08:55:18","packageid":49132,"repoid":1,"summary":"sci-biology\/bwa: Version bump to 0.7.15"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"ddedc35d1caf532d1d2aa0d1eadadee1399b0e80","committime":"2016-05-07T23:22:25","packageid":49132,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Package-Manager: portage-2.2.28","commitid":"c1fb3811426183133b6ee50bc58f03f2a90e93ca","committime":"2016-05-07T23:17:41","packageid":49132,"repoid":1,"summary":"sci-biology\/bwa: Version bump"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"945f0d2a26da4f944fd06ad6a874f69d37ce1e06","committime":"2015-08-09T09:26:46","packageid":49132,"repoid":1,"summary":"2015-08-09 09:26:21 UTC"},{"authoremail":"robbat2@gentoo.org","authorname":"Robin H. Johnson","body":"This commit represents a new era for Gentoo:\nStoring the gentoo-x86 tree in Git, as converted from CVS.\n\nThis commit is the start of the NEW history.\nAny historical data is intended to be grafted onto this point.\n\nCreation process:\n1. Take final CVS checkout snapshot\n2. Remove ALL ChangeLog* files\n3. Transform all Manifests to thin\n4. Remove empty Manifests\n5. Convert all stale $Header$\/$Id$ CVS keywords to non-expanded Git $Id$\n5.1. Do not touch files with -kb\/-ko keyword flags.\n\nSigned-off-by: Robin H. Johnson \nX-Thanks: Alec Warner - did the GSoC 2006 migration tests\nX-Thanks: Robin H. Johnson - infra guy, herding this project\nX-Thanks: Nguyen Thai Ngoc Duy - Former Gentoo developer, wrote Git features for the migration\nX-Thanks: Brian Harring - wrote much python to improve cvs2svn\nX-Thanks: Rich Freeman - validation scripts\nX-Thanks: Patrick Lauer - Gentoo dev, running new 2014 work in migration\nX-Thanks: Michał Górny - scripts, QA, nagging\nX-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed","commitid":"56bd759df1d0c750a065b8c845e93d5dfa6b549d","committime":"2015-08-08T20:49:04","packageid":49132,"repoid":1,"summary":"proj\/gentoo: Initial commit"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"a637bd65b7fef8e2be4e7fc6e9097479372e0e2e","committime":"2015-06-19T16:38:33","packageid":49132,"repoid":1,"summary":"2015-06-19 16:35:30 UTC"}],"dependencies":[{"block":false,"categoryid":396,"description":"Virtual for libz.so providers","ebuildids":[687332],"firstseen":"2025-11-04T07:31:41.418357","name":"zlib","packageid":78605}],"depending":[],"ebuilds":[{"archs":["~amd64","~x64-macos","~x86"],"ebuildid":687332,"firstseen":"2020-09-26T11:51:58.195171","license":"GPL-3","moddate":"2026-03-22T20:20:57","packageid":49132,"repoid":1,"slot":"0","uses":[],"version":"0.7.17"}],"masks":[],"package":{"categoryid":353,"description":"Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"bwa","packageid":49132},"rdependencies":[{"block":false,"categoryid":450,"description":"Larry Wall's Practical Extraction and Report Language","ebuildids":[687332],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"perl@gentoo.org","maintainername":"Gentoo Perl Project","name":"perl","packageid":44582},{"block":false,"categoryid":396,"description":"Virtual for libz.so providers","ebuildids":[687332],"firstseen":"2025-11-04T07:31:41.418357","name":"zlib","packageid":78605}],"repos":[{"branch":"master","lastcommit":"1f58741385367db432e79500a838ced67b2a773d","name":"gentoo","path":"\/usr\/portage","repoid":1,"upstream":"origin"}],"tracked":false,"urls":["https:\/\/github.com\/lh3\/bwa\/"],"uses":[]}